Atran has experimented on the ways scientists and ordinary people categorize and reason about nature,[9][10][11] on the cognitive and evolutionary psychology of religion,[12][13][14][15] His work has been widely published internationally in the popular press, and in scientific journals in a variety of disciplines. He has briefed members of the U.S. Congress and the National Security Council staff at the White House on the The Devoted Actor versus the Rational Actor in Managing World Conflict,[16] on the Comparative Anatomy and Evolution of Global Network Terrorism,[17] and on Pathways to and from Violent Extremism.[18] He was an early critic of U.S. intervention in Iraq[19] and of deepening involvement in Afghanistan.[20]

Atran has also been a staunch opponent of political attempts to eliminate government funding for social science, arguing that it is critical to the national interest, including innovation and security in business, technology, medicine and defense.[21]

He has collaborated on research on how political negotiations could be made more likely to produce agreement. Atran and the psychologists Jeremy Ginges and Douglas Medin and political scientist Khalil Shikaki conducted an experiment [26] that surveyed "600 Jewish settlers in the West Bank, more than 500 Palestinian refugees, and more than 700 Palestinian students, half of whom identified with Hamas and Palestinian Islamic Jihad."[27] The researchers divided the subjects into three groups, each of which was presented with a different "hypothetical peace deal." In the basic situation, those surveyed were presented with "a two-state solution in which the Israelis would withdraw from 99 percent of the West Bank and Gaza but would not have to absorb Palestinian refugees"; the proposal "did not go over well."[27] For the second group, the hypothetical deal "was sweetened with cash compensation from the United States and the European Union, such as a billion dollars a year for a hundred years, or a guarantee that the people would live in peace and prosperity. With these sweeteners on the table, the nonabsolutists, as expected, softened their opposition a bit. But the absolutists, forced to contemplate a taboo tradeoff, were even more disgusted, angry, and prepared to resort to violence."[28] But for the third group, the proposed two-state solution was "augmented with a purely symbolic declaration by the enemy in which it compromised on one of its sacred values."

In the deal presented to Israeli settlers, the Palestinians "would give up any claims to their right of return" or "would be required to recognize the historic and legitimate right of the Jewish people to Eretz Israel";[29] in that presented to the Palestinians, Israel "would recognize the historic and legitimate right of the Palestinians to their own state and would apologize for all wrongs done to the Palestinian people," or would "give up what they believe is their sacred right to the West Bank" or would "symbolically recognize the historic legitimacy of the right of return [without in fact granting it]".[26] In summarizing the result, cognitive psychologist Steven Pinker says, "Unlike the bribes of money or peace, the symbolic concession of a sacred value by the enemy, especially when it acknowledges a sacred value on one's own side, reduced the absolutists' anger, disgust, and willingness to endorse violence."[29]

Atran has been engaged in conflict negotiations in the Middle East[30][31][32]

His work on the ideology and social evolution of transnational terrorism, which has included fieldwork with mujahedin and supporters in Europe, the Middle East, Central and Southeast Asia, and North Africa, has challenged common assumptions. Steven Pinker summarizes some of Atran's findings thus: "Far from being ignorant, impoverished, nihilistic, or mentally ill, suicide terrorists tend to be educated, middle class, morally engaged, and free of obvious psychopathology. Atran concluded that many of the motives may be found in nepotistic altruism... [Atran shows that] Hamas and other Palestinian terrorist groups [hold] out a carrot rather than a stick to the terrorist's family in the form of generous monthly stipends, lump-sum payments, and massive prestige in the community.... Atran has [also] found that suicide terrorists can be recruited without these direct incentives. Probably the most effective call to martyrdom is the opportunity to join a happy band of brothers. Terrorist cells often begin as gangs of underemployed single young men who come together in cafes, dorms, soccer clubs, barbershops, or Internet chat rooms and suddenly find meaning in their lives by a commitment to the new platoon.... Commitment to the group is intensified by religion, not just the literal promise of paradise but the feeling of spiritual awe that comes from submerging oneself in a crusade, a calling, a vision quest, or a jihad. [Atran writes that religion] may also turn a commitment to a cause into a sacred value - a good that may not be traded off against something else, including life itself. The commitment can be further stoked by the thirst for revenge, which in the case of militant Islamism takes the form of vengeance for the harm and humiliation suffered by any Muslin anywhere on the planet at any time in history, or for symbolic affronts such as the presence of infidel soldiers on sacred Muslim soil."[33]

Atran is quoted as summarizing his work thus: "When you look at young people like the ones who grew up to blow up trains in Madrid in 2004, carried out the slaughter on the London underground in 2005, hoped to blast airliners out of the sky en route to the United States in 2006 and 2009, and journeyed far to die killing infidels in Iraq, Afghanistan, Pakistan, Yemen or Somalia; when you look at whom they idolize, how they organize, what bonds them and what drives them; then you see that what inspires the most lethal terrorists in the world today is not so much the Koran or religious teachings as a thrilling cause and call to action that promises glory and esteem in the eyes of friends, and through friends, eternal respect and remembrance in the wider world that they will never live to enjoy.... Jihad is an egalitarian, equal-opportunity employer: ...fraternal, fast-breaking, thrilling, glorious, and cool."[34]

Atran conducts ongoing research in Guatemala, Mexico, and the U.S. on universal and culture-specific aspects of biological categorization and environmental reasoning and decision making among Maya and other Native Americans.[35]

Atran's debates with Sam Harris, Dan Dennett, Richard Dawkins and others during the 2006 Beyond Belief symposium on the limits of reason and the role of religion in modern society highlight the differences between these authors, who see religion as fundamentally false and politically and socially repressive, and Atran who sees unfalsifiable but semantically absurd religious beliefs as historically critical to the formation of large-scale societies and current motivators for both conflict and cooperation.[36][37][38][39]

Atran's publications include Cognitive Foundations of Natural History: Towards an Anthropology of Science, In Gods We Trust: The Evolutionary Landscape of Religion, Plants of the Peten Itza' Maya (co-authored with Ximena Lois and Edilberto Ucan Ek), The Native Mind and the Cultural Construction of Nature (co-authored with Douglas Medin), and Talking to the Enemy: Faith, Brotherhood, and the (Un)Making of Terrorists.